This page was produced as an assignment for an
undergraduate course at Davidson College.

Yeast Gene Expression: MRS2 and YOR331C
Revisited

Introduction:

The goal of this web page is to utilize public
databases in order to find the gene expression for two types of genes using
DNA Microarrays. The species that the two genes will be analyzed from is Saccharomyces
cerevisiae. One annotated gene, MRS2, and one non-annotated gene, YOR331C,
will be reevaluated using DNA microarrays found in public databases. To learn
more about the genes MRS2 and YOR331C link to the previous web assignment (Yeast
Genes).

To understand how DNA Microarrays work,
link to this page.
DNA microarrays measure the expression of every gene in the genome! With this
data, researchers can subject the genome to many different experimental conditions
and learn how the genome responds. All of the data is already waiting to be
discovered, all researchers have to do is put the pieces together to learn how
the genome works.

For the expression of genes on this web page, the
colors green and red will be used to demonstrate repression and induction respectively.
The brighter a color is, the more highly induced or repressed a gene is.

MRS2 Expression

As my previous web assignment informed, MRS2 is
a magnesium ion transporter protein in the cell membrane of mitochondria in
yeast cells. More simply, this gene encodes for an integral membrane protein
of an organelle that produces ATP for yeast cells. As a mitochondria-related
gene, it seems clear that MRS2 should be a highly regulated gene.

To begin my search for MRS2 expression, I searched
the Expression
Connection web site for MRS2. My results were not what I expected. Since
MRS2 encodes a mitochondrial ion transport gene, it seemed clear to me that
this gene would be strictly regulated since energy production is a critical
cellular function, especially under stressed conditions. One induced expression
that I found for MRS2 was the histone depletion experiment by JJ Wyrick et al
(histone
depletion).

Figure2: This graph shows the induction of MRS2 over 6 hours while
the yeast cell was histone depleted.

The graph gives a clear example of how DNA microarray data can
be used individually to show the expression of a gene under a certain experimental
condition. The rest of the figures will use only color coded lines to demonstrate
the same data in a much simpler way.

The next step to understanding various genes and their expression
in DNA Microarrays lead me to analyze various datasets with different experimental
conditions. Under different experimental conditions, MRS2 should be clustered
around similar genes with similar functions. Using this "guilt by association"
method of finding similar genes, I should be able to find various datasets that
have similar genes. Of course, the possibility that some genes share a common
promoter with MRS2 is also one possible reason for expressions to be similar.

Expressions in Histone-Depleted Genes

Figure
3: This figure shows genes that have similar expression profiles for histone-depletion.

For Figure 3, notice the diversity in the types of genes that
are presented by genes that are clustered by similar expressions. Clearly, not
all of the genes in this figure have similar functions to MRS2, however, some
similarity does exist for genes such as TRS31, HXT3, HMX1, and PUT4. All of
these genes perform some type of transport between membranes, just like MRS2,
which encodes for a magnesium ion transporter.

Expressions in Genes Undergoing Diauxic
Shift

Figure 4: This figure shows genes that have similarity in expression
to MRS2, namely in their repression under the stress of diauxic shift.

Diauxic shift is the shift from aerobic respiration to anaerobic
fermentation in yeast cells (JL DeRisi et al, 1997). Because ATP is produced
aerobically by respiration in the mitochondria and the cell is shifting towards
anerobic fermentation, the repression of MRS2 is not surprising.

Once again similar transport protein genes are clustered close
to MSR2 such as SAM3 and BET3. Also, many genes have their cellular component
in mitochondria for this clustering, such as MRPL50, ATP12, MRPL3 and SSQ1.
In this circumstance, the idea of a circuit might be one possible explanation
for the frequency that genes occur in mitochondria. The idea of a circuit involves
the presumption that certain genes might be repressed at the same time by a
certain mechanism. In this case, the diauxic shift might cause repression of
certain mitochondria-linked genes that are regulated by a circuit.

Expression in Genes Exposed to Various
Alpha Concentrations

Figure 5: This figure shows an increasing in induction when yeast
genes are exposed to various alpha concentrations.

In this figure, the data seems to give an interesting conclusion.
Only one gene's cellular component is in mitochondria and no genes are present
that have any type of transport activity. This clustering of genes with similar
expressions shows that the guilt by association idea might not always work.
Just because similar expression exists between two genes doesn't necessarily
mean that the genes share the similar functions. When trying to find a trend
in related function or similar cellular locations for genes, it seems very probable
that with 6,000 genes

From the data and results I posted in the last
web assignment, YOR331C seemed to have a very close cellular role to MRS2(Favorite
Yeast Gene). In my analysis of YOR331C using DNA microarrays, I will specifically
look for trends in the expressions of genes clustered around YOR331C under various
experiemental conditions. After I have presented the datasets, some type of
cellular role for YOR331C should be evident. Then, I should be able to comment
upon the hypothesis that MRS2 and YOR331C have similar cellular roles.

After DNA damaging elements are introduced into
the cell, the cell cycle is arrested and the cell concentrates on DNA repair.
During this type of cellular function, YOR331C is slightly induced and then
later repressed. VMA4 shows a similar expression profile. I hypothesize that
VMA4 at first carries out its normal function, transporting hydrogen until even
this cellular function is arrested and DNA repair is fully focused on.

Expression with Genes Exposed to Alpha
Factor over time

Figure 7: This figure shows genes clustered around YOR331C when
yeast cells are exposed to alpha factor over a period of 2 hours.

Alpha factor is a signaling pheromone to other yeast cells that
a particular yeast cell is interested in reproducing sexually. This expression
shows how YOR331C gives a very weak expression during the time when the cell
is exposed to alpha factor. One important gene to notice in this figure is COX15,
a gene whose cellular role is in the mitochondria. If this gene has any functional
relationship or similarity in cellular location, then YOR331C might be similar
to MRS2.

This figure shows one important gene, VMA6. Because VMA4 had one
similar expression profile, it seems likely that other VMA proteins would share
similar expression profiles for certain conditions. The idea that VMA proteins
might also share a similarity in function with YOR331C is another possibility.
NFU1 is another gene that is clustered with YOR331C that might show a similarity
in function and would support the more basic hypothesis that YOR331C is some
type of transporter. For instance, YOR331C is similar to MRS2 because it could
functionally be some type of transporter protein like NFU1 or the VMA proteins.

Expression of Genes Undergoing Sporulation

Figure 9: This figure shows the expression of genes
in yeast cells that are undergoing sporulation.

This figure reinforces the idea that VMA genes
such as VMA4 and VMA8 are linked in expression to YOR331C or perhaps linked
in function.

Further Reinforcement of VMA Gene Expression
Clustering with YOR331C

Reinforcement for similar expression between VMA
genes and YOR331C is evident under other experimental conditions. For the environmental
changes dataset, only VMA4 and YOR331C are clustered together (Environmental
Changes). This data bolsters the idea that VMA4 and YOR331C might be linked
functionally or through some type of expression mechanism that controls both
VMA genes and YOR331C. Also, viewing the experiment in which expression is regulated
by the PHO pathway shows VMA4 and VMA6 clustered with YOR331C.

Figure 10: This figure shows that VMA4 and VMA 6 are clustered
with YOR331C when expression is regulated by the PHO pathway.

Not only do the two VMA genes cluster with YOR331C in this dataset,
but these two VMA proteins are the first two that cluster with YOR331C meaning
that they have the closest correlation to YOR331C.

Because there is an overwhelming data that support the similarity
in expression between YOR331C and VMA genes, I believe that either YOR331C has
a similar cellular role to VMA genes or shares a promoter with VMA genes. Since
VMA genes are a type of ion transporter, my hypothesis that YOR331C's cellular
role is similar to MRS2's cellular role is not completely unreasonable. If YOR331C
is a hydrogen ion transporter or a transporter protein of any kind, then it
does bear some similarity to MRS2.

When further investigation is made into the chromosomal location
of VMA, the SGD database gives a physical map of chromosome XV and VMA is a
neighbor to both YOR331C and MRS2 (Physical
Map). For this reason, the idea that VMA might share a promoter with YOR331C
seems like the most plausible explanation for their similarity in expression.